Reaction Mechanisms, Pathways; Bioreactions, and Bioreactors

The next best thing to knowing something is knowing

where
to

find it.

Samuel Johnson (1 709-1784)

Overview. One of the main w a d s that tics this chapter together i s b e pseudestendy-state-hypothesis (PSSH) and the concept of active intermediates, We shall use it to develop rate laws for both chemical and biological reactions. We kgin by discussing reactions which do not follow elementary rate laws and are not zero, first, or second order. We then show how reactions of this type involve a lumber of reaction steps, each of which is elementary. After finding the net rates of reaction for each species, we invoke the PSSH to arrive at a rate Iaw that is consistent with experimental observation. After discussing gas-phase reactians, we apply the PSSH to biological reactions, with a focus on enzymatic reactions. Next, the concepts of enzymatic reactions are extend& to organisms. Here organism growth kinetics are used in modeling both batch reactors and CSTRs (chernostats). Finally. a physiological-based-phmacokinetic approach to modeling o f the human body is coupled with the enzymatic reactions to develop concentration-time trajectories for the injection of both toxic and nontoxic substances.

7.1 Active~lntermediates and Nonelementary Rate Laws

In Chapter 3 a number of simple power law models. that is,

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Reaction Mechan~srns, Pathways, Bioreactions, and Bkoreactors

Chap. 7

were presented where n was an integer of 0. 1, or 2 corresponding to a zero-,

first-. and second-order reaction. However, a large number of reactions. the orders are either noninleger such as the decomposition of acetaldehyde at 500'C

where the rate Iaw is

or of a form where there are concentration terms in both the numerator and denominator such as the formation of HBr from hydrogen and bromine

Rate laws of this form usualIy involve a number of elementary reactions and at least one active intermediate. An rxc.rhheinrrrn~ediareis a high-energy molecule that reacts virtually as fast as il is formed. As a result. it is present in very small concentrations. Active intermediates (e.g., A * ) can he formed by collision or interaction with other molecules.

Properties of

mactive
intermediate A*

Here the activation occurs when translational kinetic energy is, transferred into energy stored in internal degrees of freedom. particularly vibrational degrees of freedom.' An unstable molecule (i.e., active intermediate) ir not formed solely as a consequence of the ~nolecule moving at a high velocity (high translational kinetic energy). The energy must be absorbed into the chemical bonds where high-amplitude oscillations will lead to bond ruptures. molecular rearrangement. and decomposition. lo the absence of photochemical effects or similar phenomena. the transfer of translational enerFy to vibrational energy to produce an active ~ntermediarecan occur only as a consequence of moleciiIar
collision or interaction. Colliqion theory is discussed in the Profes.rinnal Rqfer4ence Shelf in Chapfer 3. Other types of active intermediates that can be formed are free radicals (one or more unpaired electrons. e.g., C H , . ) . ionic intermediates hg.. carbon~umionL and enzyme-substrare complexes, to mention a few. The idea of an active intermediate was first postuIared in 1922 by F. A. Lindermann2 wlio used it to explain changes i n reaction order with changes In reactant concentratic~n\.Becauae the active intermediates were zo short Lived
-.

--

\V. J. Muore. IJI~y.riccil Clr~rairir?: (Readrng. Mass,: licmgman Pi~hlishingGmup, 199s). ! F. A. 1,indermann. Trotlr. fi~mtlu\: Soc:. 17, 39X i 1922 j.
I

Sec. 7.1

Active Intermedates and Norelementary Rate Laws

379

and present in such low concentrations, their existence was not really defmitiveIy seen untiI the work of Ahmed Zewail who received the Nobel Prize in 1999 for femtosecond spectroscopyn3 H i s work on cyclobutane showed !he reaction to form two ethylene molecules did not proceed directly, as shown in Figure 7-I(a), but formed h e active intermediate shown in the small trough at the top of the energy reaction coordinate diagram in Figure 7-l(b). As discussed in Chapter 3, an estimation of [he barrier height, E, can be obtained using computational software packages such as Spartan, Cedus" or Gaussim as discussed in the Moleculur Modeling Web Module in Chapter 3.

la)

(b)

Figure 7.1

Reaction coordinate. Counesy Scierrce Nen's. 156, 247 (1999).

7.1.I Pseudo-Steadystate Hypothesis (PSSH)

In the theory of active intermediates, decomposition of the intermediate does not occur instantaneously after internaI activation of the molecvle: rather, there
is a time lag, although infinitesimally small, during which the species remains activated. Zewail's work was the first definitive proof of a gas-phase active intermediate that exists for an infinitesimally sban time. Because a reactive intermediate reacts virtualIy as fast as it is formed, the net rate of formation of an active intermediate (e.g.. A*) is zero, i.e.,
PSSH

r** = 0

(7-1 1

This condition is also referred to as the Pseudo-Steady-State Hypothesis (PSSH). If the active intermediate appears in n reactions, then

To illustrate how rate laws of this type are formed, we shall first consider the gas-phase decomposition of azomethane, AZO, to give ethane and nitrogen:

J . Pererson. S C ~ P I INPW. L * ~ 156. 247 (1999).

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Reaction Mechanisms, Pathways, Bioreadions, and Bioreactors

C I

Experimental observations4 show that the rate of formation of etha first order with respect to A 2 0 at pressures greater than 1 atm (relatively
concentrations)

and second order at pressures beIow 50 mmHg (low concentrations):

T o explain this first and second order depending on the concentratic A 2 0 we shall propose the following mechanism consisting of three ele tar), reactions.

Mechanism {Reaction 2: [(cH~),N,]" + (CH,),N,

2(CH,),N,

+ (CH,),N

In rencrion I, two AZO molecules collide and the kinetic energy of one . molecule is transferred to internal rotational and vibrational energies o other AZO molecule, and it becomes activated and highly reactive AZO*}). In reaction 2, the activated molecule (AZO*) is deactivated thrl collision with another AZO by transferring its internal energy to increasl kinetic energy of the mdecutes with which AZO* collides. In reacrbn 3, high activated AZO* molecule, which is wildly vibrating, spontanec decomposes into ethane and nitrogen. Because each of the reaction ste elementary. the corresponding rate laws for the active intermediate AZC reactions ( l ) , (21, md (3) are
Note: The specific reaction rates, k, are all defined w n the active intermediate AZO*.

(1)

(2)

(3)

These rate laws [Equations (7-3) through (7-5)] are pretty much us' in the design of any reaction system because the concentration of the a intermediate AZO* is not readily measurable. Consequently, we will us< Pseudo-Steady-State-Hypothesis (PSSH)to obtain a rate law in terms of I surable concentrations. We first write the rate of formation of product (with k, = k,,,,)

H .C. Ramsperget, J. Am. Chcrn. Soc., 49, 912 (1927).

Sec. 7.1

Active Intermediates and Nonelernentary Rate Laws

381

To find the concentration of the active intermediate AZO*, we set the net rate of AZOX equal to zcro,' r,,,, = 0.

=k

l~izo - k~CAzo~CAzo-A-,CAzo~ =0

Solving for CAZQ*

Substituting Equarion (7-8) into Equation (7-6)

At low AZO concentrations,

for which case we obtain the following second-order rate law:

Ar high concentrations

in which case the rate expression fotlows first-order kinetics,

In describing reaction orders for this equation, one would say the reaction is apparent firsf order at high azornethane concentrations and apparent second order at low azomethsne concentrations. The PSSH can also explain why one observes so many first-order reactions such as

"or

further elaboration on this secrion. see R.Ark. Am. Sci., 38, 419 ( 19701,

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Reaction Mechanisms, Pathways, Bioreaclions, and Bioreactors

Chap. 7

SymbolicaIly this reaction will be represented as A going to product P, that is,

A+P
with

The reaction is first order but the reaction is not elementary. The reaction proceeds by first forming an active intermediate, A*, from the collision of the reactant molecule and 'an inert molecule of M. Either this wildly oscillating active intermediate is deactivated by collision with inen. M, or it decomposes to form product.

Reaction pathways

The mechanism consists of the three elementary reactions:

Activation

(1)

A+M

*I

A*+M

Deactivation

(2) A' + M

~ecorn~os'ition(3)

'' > A +M A* i ' P

Writing the rate of formation of product

and using the PSSH to find the concentrations of A* in a manner similar to the azomethane decomposition described earlier, the rate law can be shown to be

Because the concentration of the inert M is constant. we let

to obtain the first-order rate law

-rA = CCA

Sec. 7.1

Aniva lntermediafes and Nonelementarj Rate Laws

First-order rate law for a nonelementary reaction

Consequently, we see the reaction

A+P follows an elementary rate law but is not an elementary reaction.

7.1.2 Searching for a Mechanism

In many instances the rate data are correlated before a mechanism is found. It is a normal procedure to reduce the additive constant in the denominator to 1. We therefore divide the numerator and denominator of Equation (7-9) by k3 to obtain

General Considerations. The rules of thumb listed in Table 7-1 may be of some help in the devciopment of a mechanism that is consistent with the experin~entalrate law. Upon application of Table 7-1 to the azomethane example just discussed. we see the following from rate equation (7-12):
1. The active intemediate. AZO*. collides with azomethane. AZO [Reaction 21. resulting in the concentration of AZO in the denorninator. 2. AZO* decomposes spontaneously [Reaction 31, resulting in a constant in the denominator of the rate expression. 3. The appearance of AZO in the numerator suggests that the active intermediate AZO* is formed from AZO. Referring z o Reartion 1, we see that this case is indeed true.
- - --

.!A

I . Species having the concentraricm[s) appearing in the detinminaror of the rate law probably collide with the active intermediate, for example,
.4 -t A * + [Collision products]

2. If a constant appears i n the ~lcnornitrator, one of the reaction neps is probably the spontaneous decomposition of the active intermediate. for example.
A*

3. Species having the concentration(s) appearing in the numerator of the sate

law probably produce the active intermediate in one of the reaction steps. for

[Decompasition products]

example,
[reactant]

---+

A * t- (Other products]

Finding the Reaction Mechanism. Now that a rate law has been synthesized from the experimentai data, we shall try to propose a mechanism that is consistent with this rate law. The method of artack will be as given in Table 7-2.

384
- --

Reaction Mechanisms, Pathways. Bioreactions, and Bioreactors

Cr

Once the rate law is found, the search for the mechanism begins.

rate law obtained from experimei data, if possible. 3. Model each reaction in the mechanism sequence as an elementary reacti 4. After writing rate Iaws for the rate of formation of desired product, w the rate laws for each of the active intermediates. 5 . Use the PSSH. 6. Eliminate the concentration of the intermediate species in the rate laws solving the simultaneous equations developed in Steps 4 and 5 . 7.If the derived rate law does not agree with experimental observat assume a new mechanism andor intermediates and gc~ to Step 3 . A szn background in organic and inorganic chemistry is helpful in predicting activated intermediates for the reaction under consideration.

I . Assume an active intermediate(5). 2. Postulate a mechanism. utilizing the

Example 7-1
Collapsing
cavitation microbubble

The Stern-Volmer Equatiu ion

-- --Liquid

Light is given off when a high-intensity ultrasonic wave is applied to water' light results f r o m microsize gas bubbles (0.1 mm) being formed by the ulta wave and then being compressed by it. During the compression stage of the the contents o f the bubble (e.g., water and whatever else is dissolved in the t . g . . CS,, Ot, N , ) are compressed adiabatically. This rornpression gives rise to high temperatures and k~netic energies r gas molecules, which through molecular collisions generate active intermediate cause chemical reactions to occur in the bubble.

The intensity of the light given off. I, is proportional to the rate of deactivati an activated water moleculr that has been formed in the rnicmbubble.

Light intensity (I) x ( - r ti20,) = kc,,1o. An order-of-magnitude increase in the intensity of sonofuminescer observed when either carbon disulfide or carbon tetrachloride is added to the The intensity of Iuminescence, I, for the reaction

A similar result exists for CC1,.

P . K. Chendke and H. S. Fogler, J. Phys.

Chem., 87, 1362 (1983).

Sec 7.t

Rctrve Int~rmediatesand Nonelementary Rate Laws

385

However, when nn alrphatic alcohol, X. is added to the solution, the intensity decreases with increa\ing concentration of alcohol. The data are usually reported in tern? nf a Stern-Volrner plot in which relat~vcilltensity is given as a function of alcohol concentration, C ., (See Figure E7-1.1, where 1,) is the sanoluminescence ~ntensity in the absence of alcohol and I is the sonoluminescence intensity in the presence of alcohol.) Suggest a mechanism consistent with erperimental observation.

Stem-Volmer plot

cx(krnol/m3)
Figure E7-1.1 Ratio of luminescence intensities as a function of Scavenger concentration.

From the linear plot we know that

where C , = (X). Inverting yieIds

From rule 1 of Tabte 7-1, the denominator suggests that alcohol the active intermediate:

(X)collides with
(E7I .3)

X
Reaction Pathways

+ Intermediate + Deactivation products

The alcohol acts as what is called a scavenger to deactivate the active intermediate. The fact that the addition of CCI, or CS? increases the intensity of the luminescence.

lead? us to postulate (rule 3 of Table 7 - I ) that the active intermediate was probably formed from CS,:
M + CS2

CS;
etc.).

+M

where

M is a third body {CS?, H 2 0 , N : ,

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Reabton Mechanisms, Pathways, Bioreactiom, and Biomactors

Chap. 7

We also know that deactivation can occur by the reverse of Reaction (E7I -5). Combining this information, we have as our mechanism:

Activation:
The mechanism

M M X

+ CS2
+ CS;
+ CS;
CS;

CS; + M
CS2

(E7-1.5)
(E7-1.6) (E71.3)
(E7-1.7)

Deactivation: Deactivation:
Luminescence:

+M

CSZ + X

CS, + hv

I = lE,(CS;)
Using the PSSH on CS; yields
r,,;
=0=

(E7-2.8)

I C S : ) ( M f - L:(CS;)(M) - k,(X\(CS:) - k4(CS;)

Solving for CS; and substituting into Equation (E7-1.8) gives us I=

k4 k , (CS,)(W k, (M) + k, (X) + k,

In the absence of alcohol,

For constant concentrations of CS, and the third M y , M, we take a ratio of Equation (E7l . 10) to (E7- 1.9):

5 = 1+ 3 ' I k2(")+

k4

(X) = I + X1(X)

which i s of the same form as that suggested by Figure E7-1 . l . Equation (E7-1.11) and similar equations involving scavengers are called Sfern-Volmcr equations. A discussion of luminescence is continued on the CD-ROM Web Module. Glow Sticks. Here, the PSSH ts applied to glow sticks. First, a mechani~mfor the reacttons and luminescence i s developed. Next, mole balance equations are written on each species and coupled with rate law obtained using the PSSH and the resulring equations are solved and compared with experimental data.
Glow sticks

3.1.3 Chain Reactions

Now, let us proceed to some slightly more complex examples involving chain reactions. A chain reaction consists of the following sequence:

Step? i n a chain
reaction

1 . Iniriarion: formation of an active intermediate. 2. PE-opugurionor chai~ltrnng~r: interaction of an active intermediate with the reactant or product to produce another active intermediate. 3. Tcrrinnfinn: deactivation of the active intermediate to form products.

Sec. 7.1

Active Intermediates and Nonelementary Rate Laws

387

/
I

Example 7-2 PSSH Applied to Thermal Cracking o f Ethane

The thermal decomposition of ethane to ethylene, methane, butane, and hydrogen is believed to proceed in the following sequence:
Initiation:
(1)

CzHd % 2CH,*

r ~ ~ 2 % - k ~ ~ iCzH63 2 ~ 6

(4)

H*+C2H6- 4

C2Hs*+H2

r4c,1~, =

-k4 [H I[C?

H61

Termination:

(a) Use [he PSSH to derive a rate law for the rate of formation of ethylene. (b) Compare the PSSH solution in Part fa) to that obtained by solving the complete ser of ODE mole balances.

Solution

Part (a) Developing thc Rate Inw

The rate of formation of ethylene (Reaction 3) is

Given the f~llowingreaction sequence: For the active intermediates: CH,* , Cz1-1,. ,H the net rates of reaction are

From reaction stoichiornetry we have

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Reaction Mechanisms. Pathways, Bioreactions, and Bioreactors

Ch,

Substituting the concentrations into rhe elementary Equation (E7-2.4) gives

2kI[CIHh ] kZICH1 ][C2Hh]= 0 Solving for the concentration uf the Free radical [CH,- ] ,

(El

Adding Equations (E7-2.2) and tE7-2.3 t yields

-

1 A I~ - 5 ~~ : " 5 *~ =

~ 0

Substituting for concentrationr in the rate laws kI[CH3a J[C2H6]-k5[C2Hr*12 = 0

PSSH solution

Solving for [ C, H,

] gives us

, ,r

H~ ] =

{x.
I;,

[CH,

][C, H6I}[I2 =

{% [C2H61}
' 8 5

CIZ

(E7

Substituting for C2H,min Equation (E7-2.1) yields the rate of formation of ethj

Next we write the net rate of

H formation in Equation (E7-2.3) in terms of

centration
k 3 [ C : H 5 * ] - k 4 [H*lICtHbl = Q

Using Equat~on(E7-2.8) to substitute for (C2H, m ) gives the concentration o hydrogen radical

The rate of disappearance OF ethane is

r=2~6

=-k,[C,H,]-k2[CH,m][ClH6]-k4[H*1[C2N61 (E7-

Substituting for the concentration of free mdicats. the nte law of disappearan1 ethane is

Sec. 7.1

Ac!ive Intermediates and Nonelementary Rate Laws

389

For a constant-volume b ~ t c h reactor, the combined mtlle balilnces and rate laws for disappearance of ethane ( P I ) and the tormatlo~rnf ethylene (PSI are

Combined mole balance and rate law using rhe PSSH

The P in P I (i.e., Cpl1 and P5 (i.e.. C,,) is to remind us rhat we have used the PSSH in arriving ar these balances. At 1000 K the specific reaction rates are C I = 1.5 X 10-I s-', k2 = 2.3 X 10h drn'lmol +s, k, = 5.71 X 1I)' s-[. k, = 4.53 X I V dm31rnol.s. and k, = 3.98 x IOV dtnVmol .s. For an entering ethane concentration of 0.1 molldm' and a temperature of 1 0 0 K, Equations (E7-2.13) and (E7-1.14) were solved and the concentrations of ethane. Cp,, and ethylene, C,,. are <tiown a s a fi~nction of time in Figures E7-2.2 and E7-2.3. In developing this cancentntion-time relationship. we used PSSH. However. we can now utilize the techniques described in Chapter 6 to solve the full set of equatiuns For ethane cracking and then compare these results with the much simpler
PSSH solutions.

Part (bl Testing the PSSH for Ukame Cracking

The thermal cracking of ethane i s believed to ofcur by the reaction sequence given in Part (a). The speo~fc reaction rates are given as a function of temperature:

Part (b): Carry out mole baiance on every species, solve. and then plot the concentrations o f ethane and ethylene as a function o f time and compare with the PSSH concentration-time measurements. The initial concentration of ethane i s 0.1 molldm-' and the temperature i s 1 0 K.

Let I = C2H6, 2 = CHJm, 3 = CH4. 4 = C2H59, 5 = C2H4, 6 = H-, 7 = H2, and 8 = C4Hlo. The combined mole balances and rate laws become

(C2H6): 5 =-klC~-k2ClCI-k4ClCn
dr

(E7-2.15)

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Reaction Mechanisms, Pathways, Bloreactions, and Biowacrors

Chap. 7

(CH.):

= kzClC2

(E7-2.17)

(CzH,m):

5 = k 2 ~ , ~ 2 - k 3 ~ , i & ~ l ~ 6 - k 5(E7-2.18) ~: dr 5 = k3C4 dr

(E7-2.19)

(C2HA:

(H*):

dt

dC6 =k3C4-k4C,C,

(E7-2.20)

(c4 H,~): 5 dr

=!

(E7-2.22)

The Polymath program is given in Table E7-2.1.

TABLE E7-2.1.
POLYMATH PROGRAM

Figure E7-2.1 shows the cnncentration time trajectory for CH, (i.e.. Cz3. One notes a flat plateau where the PSSH is valid. Figure E7-2.2 shows a comparison of the concentration-time trajectory for ethane calculated from the PSSH (Cp,)with the ethane trajectoy (C,) calculated f r o m solving the mole balance Equations (E7-2.131 through (E7-2.22). Figure E7-2.3 shows a similar comparison for ethylene C () , and (C5).One notes that the curves are identical, indicating the va3idity of the PSSH under these conditions. Flgure E7-2.4 shows a comparison of rhe concentration-time trajector~esfor methane (C,) and butane (C,). Problem P7-2(a) explores the temperature for which the PSSH is valid for the cracking of ethane.

See. 7.1

Active Intermediates and Nonelememary Rate Laws

Note: Curves for C,and Cp, are

vinually identical.

0.020
D m

Key:

C,
1(d 12

CP

0.000

3 . m

6 CQU

9.m 12.W 15.0K1

Flgure E7-2.1 Concentntion o f active intermediate CH,*as n function of lime.

FEgure E7-2.2 Cornpanson of concentration-time trajectorieq for ethane.

Note: Curves for

C 5 and Cps

are

virtually idenlical.

Key:

(3
0.000 3 . m 6 . m 8.000 12.000 15.000 Figure E 7 1 2 . 4 Comparison of concentration-time frajecioriesfor methane tC3) and butane (C,),

0000

30M1

6[XX)

9.000 1 Z W 1 5 . W

Figure E7-2.3 Comparison o f concentration-time trajectop for

ethylene

7.1.4 Reaction Pathways

Reaction pathways help see the connection of all interacting species for multiple reactions. We hare already seen two relatively simple reaction pathways, one to explain the first-order rate law, -rA = kcA. (M + A + A * + M) and one for the ~onolurninescenceof CS, in Example 7-1. We now will develop reaction pathways for ethane cracking and for smog generation.

cd>qI,

Figure 7-2

Pa1hu.a~of erhane cracking.

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Reactron Mechanisms, Pathways, Dioreaclions, and Bioreaclors

Chi

Ethnne Cracking. With the increase in cotnputing power. more and rr analyses involving free-radical reactions as intermediates are carried out u: the coupled set? of differential equations (cf. Example 7-2). The key in such analyses is to identify which intermediate reactions are important in overall sequence in predicting the end products. Once the key reactions identified. one can sketch the parhways in a manner similar to that shown the ethane cracking in Example 7-2 where Reactions 1 through 5 are show1 Figure 7-2. Smog Formation. In Chapter 1, Problem PI 14. in the CD-ROM Sr Web hIoduIe, we discussed a very simple model for smog removal in the L hasun by a Santa Ana wind. We wiH now look a little deeper into the chemi of smog formation. Nitrogen and oxygen react to form nitric oxide in the inder of au~omobile engines. The NO from automobile exhaust is oxidize1 NO2 in the presence of peroxide radicals.

Nitrogen dioxide is then decomposed photochemicaliy to give nascent 0x9

which reacts to form ozone

The ozone then becomes involved in a whole series of reactions with hy carbons in the atmosphere to form aldehydes, various free radicals, and o intermediates. which react further to produce undesirable products in pollution:

Ozone -t Olefin

+Aldehydes + Free radicals

' h RCHO + 0

0, + RCHeCHR

+ HCO

One specific example i s the reaction of ozone with I3-butadiene to f acroIein and formaldehyde, which ace severe eye irritants.
Eye tmtants

20, + CH2=CHCH=CH2
3

,,"
k,

> CH,=CHCHO

+ HCHO

By regenerating NOz, more ozone can be formed and the cycle continued. ' regeneration may be accomplished through the reaction of NO with the

Sec. 7.1

Active lntsrmediares and Nooelementary

Rate Laws

393

radicals i n the atrnorphere Reaction ( R 1). For example. thc free radical formed in Reaction (R4) can react with O2 to give the peroxy free radical.

The coupling o f the preceding reactions is shown schematically in Figure 7-3. We see that the cycle has h e n completed and that w f th a relatively small amount of nitrogen oxide, a large amount of pollutants can be produced. OF course. many other reactions are taking place. so do not be misled by the bcevity of the preceding discussion: i t does, however, serve to present, in rough outline, the role of nitrogen oxides in air pollution.

Fi~tlre 7-3 Reaction pathways in smog formation.

Metabolic Pathways. Reaction pathways find their greatest use in metabolic pathways where the various steps are ca.talyzed by enzymes. The metaboiism o f alcohol is catalyzed by a different enzyme in each step.

Alcohol Dehydrogenase

NADH

Acetaldehyde Dehydrogenase